Rurouni Kenshin Cross-Over: Prelude to a New Trouble!
by misspumpkinfreak
Summary: What if Kaoru wasn't really Kaoru? What if Misao never existed? Will they still be able to live with the people they love if they knew that something from their past threatens the lives of the people they care? A battle that will determine Japan's future; the battle of the strong will power. Misao and Kaoru learns that their destiny has been written by the Gods since their birth.
1. Chapter 1: Tomoko's Plight

So, I have been thinking whether or not I will write a fanfic about Kenshin and Kaoru and the rest but as I read other fanfics, I really don't know why Tomoe and Kaoru and demonized by many writers. In my opinion, these two women are compatible with Kenshin because he had a different attitude during the Bakumatsu and the Meiji era. I made this story as a cross-over of many different characters from other anime that some of you will recognize. I will combine some elements from RK manga as well as from the anime. Alright! This is my first time writing a really long fanfic about Kenshin and Kaoru that's why I need motivations and reviews please! Love you all! :* ("\ (*_*x)/")

 **CHAPTER ONE (Tomoko's Plight)**

 **20 March, 2016 Sunday 9pm**

 _"I see her now! After her!" roared a harsh older male voice throughout the streets. His fellow henchmen seemed to get excited chasing the small lithe figure of a young woman running desperately across the streets in search for refuge. The busy streets of Tokyo seemed uncaring and unmarred by the small crime occurring in its narrow and dark alleys. Like most of its citizens who decided to ignore the plight of the maiden in distress. The woman's name was Tomoko, a student of the Jonan Academy. Her hair was scattered throughout her face; her uniform dirty and disheveled. She gasped for breath as she tried to escape the men who were chasing after her ever since she acquired the book of the Universe of the Four Gods. She searched for places to hide, her mind wandering but still her body ran on its own accord to shelter itself from the pouring rain. She was very hungry although it was not surprising since she barely touched her food before she left the canteen two hours ago. Tomoko protected the book with her body; embracing it as tightly as possible to shelter it from the rain. She knew the book's history from Miaka and Yui; the two female students who became the priestesses of Suzaku and Seiryuu upon entering the book. At first she did not believed it, dismissing it as a trash fantasy story of the two girls. As a history lover, Tomoko is fascinated with the tales from ancient China, Japan, and Korea. Thus, being a history geek is her life-long dream that brought her delight in the past…but not now._

 _The moment Miaka gave her the book to help her with her studies, she noticed something ominous and powerful being enveloped her. But again, being the rational person, Tomoko never believed it and continued translating the book on her own. As of this moment, Tomoko had already translated the first volume of it in Japanese. The rest of the story remains in ancient Chinese texts because of the aging pages of the book. The ink was smeared and the decay of the papers continuously destroys the rest of the paragraphs. One day while she was busy deciphering the smeared characters, Tomoko noticed two men standing solemnly at the park. They were dressed in ancient Chinese costumes of the working class. Their hair was tied in a top-knot; their faces grim and lascivious. "Must be a bunch of Kung-Fu cosplayers." Tomoko muttered to herself and removed her gaze from the men who still remained focused on her. The days became weeks, and eventually months. Tomoko's favorite place is the school garden because it relaxes her and it gives her the quietness she needs to read the book. She became used to the men following her, and being the honest person, Tomoko remembered her grandfather's saying: "Never judge a person by their looks" and she strongly obeyed these words as her credo. She never suspected anything and remained focused on her goal: to preserve the book and to establish herself as a prominent author and historian. The flash of the lightning accompanied by the roaring thunder woke Tomoko from her reminiscing of the past. Amidst the rain, she can still hear the footsteps chasing after her, those men she refused to judge, want her dead now so that they can revive the Holy Tenko, that is what she heard from them. "Just who the hell is that Tenko guy! Why do they chase me?! What have I done wrong to them? Someone tell me please!" Tomoko screamed out loud; hoping that her voice might reach someone's heart and help her with the situation she's in. For quite a long time, she let her feet take her to various streets, alleys; passing various houses. Tomoko did not care. All she needs right now is to rest her feet and drink lots of cold water to quench her thirst. At last! She thought to herself. It seemed peaceful now and awfully quiet. Tomoko allowed herself to slump on to the stone pavement of a temple or some sort of a traditional Japanese style house. The wooden plaque beside the great wooden gate bore a sign: Kamiya Kasshin Ryu Dojo. A dojo huh? Will they help me and let me stay for the night until daylight? She thought a bit tired. Her eyes were filled with tears as her tired body, fear, and confusion melted into her being. The moon shone brightly, illuminating the surroundings around her. And then…the familiar sound of the men chasing her filled her thoughts once more. They have found her! Somebody help me please! Her mind trapped the scream within her throat; the words unable to escape her lips. Suddenly, the book that she has been clutching tightly all along the tiresome journey shone with a bright white light. A faint sound of a male voice, accompanied by a soft roar of the tiger was the only thing she heard before she fell into a deep sleep._


	2. Chapter 2: Tomoko and Kaoru

**CHAPTER TWO**

 *****Author's note:** _ **After the Bakumatsu ended, the Meiji Period began in 1868; from 1868 up to 1877, Kenshin wandered throughout Japan for ten long years before meeting with Kaoru. Then in the final manga, Vol. 28 Chapter 254-255, Kenshin and Kaoru got married and had a son named Kenji; this happened in the 15th year of Meiji (1882). But five years is certainly a long time and I wondered what they did from 1878 to 1881or how they ended up together. This chapter is my own take to fill the five year gap in the story. So let us begin our journey to the…**_

 _ **20th day of March, 11th year of Meiji (1878)**_

Kaoru sat on the porch of the Kamiya dojo. Like the previous years, the place is awfully quiet this time now that its former residents and visitors went on separate journeys in life. The mild spring sunshine is shining cheerily as if the sun is trying to make her happy despite her loneliness. Kaoru missed Sanosuke's visits and his usual attitude of leaching off money from her. Although she hated his shameless attitude sometimes, Kaoru never hesitated to lend him little money from her own savings. Sanosuke treated her as his younger sister and she remembered that he told her a bit of his past after they had a small talk about his family. She learned that he once lived in a small village in Shinshuu and that he had a small brother and a little sister whom he abandoned when he joined the Sekihotai army. His father was the only person who cares about them right now. Sanosuke said nothing when she asked him about his feelings; whether he feels lonely and sad leaving his family. Kaoru and Yahiko understood his silence and did not pursue the topic anymore. Right after the Jinchuu incident, Sanosuke left the group and headed towards the world. On the other hand, Yahiko inherited Sanosuke's flat and stayed there for good. Megumi left for Aizu to search for her family; Misao and Aoshi left for Kyoto as well. In the end, only Kaoru and Kenshin are the only ones left to stay at the Kamiya dojo. _That's not a farewell but a setting off…not the end but the beginning…So it is a little lonely but we have to endure it._ Kaoru remembered Kenshin's words in her reverie. Kenshin… although they became close towards one another after Enishi's fight, Kaoru can still detect Kenshin's remoteness towards her. When they are alone, Kenshin usually smiles and says nothing; he dons the goofy demeanor for Ayame and Suzume who always came to visit him every day. Ayame is already attending school for young girls and boys while Suzume still spends a lot of her time bugging the old and kind Dr. Gensai. But when they have time, they frequently pay a visit together with Yahiko at the dojo. Kaoru never wanted to be lonely anymore, but here again; she cannot help but become lonelier. Kenshin went to Kyoto to visit his dead wife's grave. Kaoru knew that even if he doesn't say it, Kenshin still loved Tomoe dearly. She still feels sadness towards Kenshin and Tomoe's fate. She always wanted Kenshin to become happy and live his life to the fullest; but because of the guilt, Kenshin still refuses to forgive himself and bears the death of Tomoe in his life. The wind blew gently towards Kaoru's face, stroking her cheek with its gust. Kaoru looked up the sky and silently wished. _I want Kenshin to be happy always…_ she stood up and clasped her hands together, eyes closed. The rest of her wish remained in her heart. After that, she smiled and went towards the main gate of the house. Suddenly, Kaoru felt a presence that made her scared. Upon opening the main door of the house, she found the body of a girl lying outside wearing odd Western clothing. Her appearance told Kaoru that the girl probably went in some sort of trouble with gangsters and managed to escape their clutches; hence, the disheveled appearance and the muddy cheeks. Kaoru recovering from her shock, screamed for help. But no neighbors came. _If only Kenshin is here! He might know what to do with her!_ Kaoru wasted no time and helped the girl inside the dojo.

 _Footsteps chased her amidst the heavy downpour of rain. Their voices harsh and cruel; their lecherous smile glittered in the darkness. She screamed on top of her lungs, running frantically; begging someone to help her. Clutching the book protectively, she braced herself to run further until she can find a place where she can rest. Of all people, she knew what would happen if the book falls onto the hands of wrong people. "Hold it right there, you brat! Just wait 'til we catch you we will feast ourselves before tearing your body to pieces!" one of the men chasing her echoed and the sound of his demonic maniacal laughter followed afterwards. Her mind froze in fear but despite that, her feet continued to run forward, never looking back. Help me please! Someone help me!_

"Someone help me! Please someone help me! I beg you please!" Tears flowed from her eyes as she scrambled frantically. She imagined herself lying on something soft and warm. Then two warm hands prevented her from moving up. She screamed again. "Help me! Please don't kill me! I beg you!" She kicked back and forth. "Will you stop that?! Here I am helping you and I get kicked in return?" An angry voice coming from a young woman stopped her. Then, she slowly opened her eyes and looked at the owner of the voice. She's right. She saw a woman probably about her age, a beautiful woman in fact; with long flowing blue-black hair and piercing blue eyes. She was wearing a yellow kimono adorned with red and orange patches and dotted with green sakura petals. She wore her hair in a ponytail tied with a green silk ribbon.

"It is rude to stare you know." The young woman interrupted her again.

"I-I-I'm s-sorry!" She bowed her head lower inwardly cursing herself for stammering, blushing from embarrassment. But nevertheless, she forced her head up to face her benefactor. It is the least she can do to thank her from saving her from the bad guys. "I'm s-sorry, yet, I am really thankful that you s-saved me from them."

"Saved you? From whom?" the woman's eyes narrowed. "What is your name?" she asked.

 _Should I give her my name?_ She thought to herself. _But it looks like she's not a bad person since she helped me and let me stay inside her home._ "My name is Tomoko. Sugioka Tomoko. 17 years old, currently attending Jonan High!" She bowed her head once more and continued. "Thank you so much for saving me, I hope to repay your generosity but in order to do that, may I borrow your phone for a while? It is okay if you do not have a credit I have my Wi-Fi dongle with me!"

"Wi-Fi? What is that?" the woman asked, confused.

Tomoko looked up. "Eh? Wi-Fi! As in internet connection that allows you to surf Facebook and YouTube on phone!"

Kaoru made a funny face. For a second, Tomoko looked around her. The walls of the house were built with wood. There is a wooden well outside covered with wood as well. A small chime hung from the porch's roof. _A traditional Japanese house indeed_. Behind Kaoru, Tomoko saw the wooden plaque that bore the same name outside the gate. Kamiya Kasshin Ryu. But there's something wrong; definitely.

"Do you have a phone?" Tomoko asked.

"Huh? A what?" Kaoru replied, puzzled.

"Or what about a PC? I need to make a report to the police. I need to send them an email so I can go out safely. I don't know but they are still probably looking for me. My brother is working for the police."

"Hey hang in there. I do not understand what you are trying to say but if you need a police their station is in town and I can accompany you if you like. And what is a PC and email? Are they your enemies?"

 _Huh? What? She didn't know email and PC! I thought all people know them by now. It's 2016!_ Tomoko's gut twisted and she suddenly has this nagging feeling that something weird definitely happened. She asked once more to confirm her suspicions. "Ummm…May I know the date...the date today?"

Kaoru's look got weirder. "March 20th."

"What is the year?"

"1878."

Tomoko's face went pale. Sweat drops formed on her face. Her expression horrified. On the other hand, Kaoru held the same expression too. "No way!" she muttered before collapsing back to the futon again.


	3. Chapter 3: The Two's Bond

**CHAPTER THREE**

"Whaaaaaaaattt?!" Outside the dojo, the dog screeched and ran away from the place upon hearing the shout of the feisty young woman inside.

"Please Miss Kamiya, I know this is hard to believe but this is not the time in which I live!"

"Are you saying that you came from the future?!" Kaoru made a disgusted facial expression and muttered. "Am I hallucinating or something?" she turned her head back and forth in a comical way.

"Oh gosh please! That is my line too! I am from 2016. I am very rational that is why I cannot believe myself that I time-traveled from Heisei to the Meiji Era!"

"2016? But this is the 11th year of the Meiji!" Kaoru peered at Tomoko closely, trying to detect whether the newcomer is telling the truth. Tomoko confronted Kaoru's gaze with her own. She needed to convince her that she was indeed from the 2016. _Aha! I can! I just need to show her my items!_ It is now or never. Tomoko asked Kaoru whether she found anything from the pockets of her school uniform. Kaoru showed her the way outside, leading to the wooden laundry line. Tomoko saw her uniform hanging neatly. "Stay there." Kaoru ordered. She and Kaoru are currently inside the living room of the house. The inside was covered with green paint and the fusuma are brilliantly covered with designs from nature. Tomoko saw Kaoru produced a small wooden bowl from the alcove. She immediately went to the table and showed her the items she recovered from her pockets.

"I do not know these items but I presumed they are important to you so I stored them."

Tomoko felt her eyes soaked. It seemed a long time since she saw the things familiar to her. Inside the bowl are her iPhone, earplugs, power bank, cords, wallet, ID's, and keys. She dipped her hand inside the bowl to get the phone. This is her chance to prove her that she is a person from the future!

"Miss Kamiya, have you seen a book? It is an old book but it is important for me. May I have it please?" Tomoko pleaded.

"Book? I did not saw any book. Not at least. Perhaps you dropped it. The only ones I saw while you were unconscious are these things." She said, gesturing to the items inside the wooden bowl.

Tomoko's face paled again and felt fear. Miaka and Yui had always reminded her not to lose the book because it contained the powers of the Four Gods. It also dawned to Tomoko that somehow, she needed to get that book as soon as possible and return it to Miaka and Yui. "How come? I just had it! I embraced that book so it will not be taken away!" She sobbed hysterically. "I need to find that book, so I can return to my time. I believe that book can bring me back to where I belong!"

Despite her suspicions, Kaoru somehow understood that the young woman needed someone to take care of her. She seemed not a bad person and her straight-forward honest eyes reminded her of Tsubame. She has the same haircut as well. When Kaoru saw her tears as she touched the weird rectangular object, she knew that somehow, no matter how ridiculous her story is, she needed her protection as a local citizen from the Meiji era. If she was truly from another time, making her wander aimlessly will only lead up to suffering and other horrible things. Kaoru smiled gently and said: "If you came from the future, you have to stay here. I will not let you wander around. Meiji period is pretty dangerous especially for a woman like you. I will help you in all the ways I can. I just don't know how but I will lend you a hand. So don't worry, Tomoko."

Tomoko's tears became more prominent; her sobs grew louder. For a long time, she needed someone to understand her and she found that in Miss Kamiya. Her blue-eyes are now gentle; she went to Tomoko's side and embraced her as if she were her beloved sister. Tomoko hugged her back and felt at home after a long journey from hell.

"Tomoko, in order for me to help you, will please tell me what happened and how come you were transported here in my time?" Kaoru asked.

Tomoko hiccupped but eventually removed herself from Miss Kamiya's embrace. She proceeded to tell her about herself.

"Like I said before, I am a student from Jonan High. I have friends too; their names were Miaka and Yui. We both study at the same school as well."

"Did they know your predicament? That you traveled back in the Meiji Era?"

"I think they do not know it. But they once told me that they became priestesses when they entered the Universe of the Four Gods. That is the title of the book I am referring to."

"So you mean that in the 21st century, people will have magical powers?" Kaoru stated, horrified at thought.

"No. At least not in terms of magic. We live in an era where we use the scientific innovations to make our lives productive. That book was only a coincidence. According to my comrades, they went to the library and Miaka saw a red phoenix flew towards the library room. And then, she and Yui were transported to Ancient China to become priestesses."

"How did a book as powerful as that came into your possession?"

"That is the answer we do not know. All I know is that I need to recover that book as soon as possible. That book is important because it is not an ordinary book. I have put my life on the line because there are people who desired to have much power and they see that book as a method of conquering the world." Tomoko stood up; determination evident in her eyes. "I cannot allow that to happen."

Kaoru nodded to her. "I will help you but let us make some food. We cannot think on an empty stomach if we don't eat anything."

Tomoko's stomach growled. "Yes, I agree with you."

The two girls headed towards the kitchen afterwards.


	4. Chapter 4: The Decision

**Author's Note:** I am sorry for those who are still waiting for Kenshin's arrival. Let him rest for a while, you know he's still tired from the Jinchu stuff. But I will introduce him and the other gangs later on. I just wanted to establish the sequence of events first. Click that 'Review' button down there! I'd love to read your messages about my story. Arigato de gozaru, minna-san! (*_^x)

 **CHAPTER FOUR**

Miss Kamiya insisted that Tomoko should address her by her first name reasoning out that it makes her feel old and isolated when she hears 'miss.' I have a companion here at the dojo but he is not here at the moment but it freaks me out whenever he calls me 'Miss Kaoru.'" She remembered her saying after her outburst. Like her former assumption, it turns out that Kaoru is also the same age like her. She is 17 and the current assistant master of the Kamiya Kasshin Style, which according to her father, is a sword technique meant for protecting people. She and Kaoru had already bonded together like real siblings; she showed her around the house and even gave her swordsmanship lessons so that she can defend herself once the goons' shows up again. In return, Tomoko let Kaoru explore her stuff. She showed her the latest technology in the future called 'smartphones.' Thanks to these gadgets, she was able to prove herself to Kaoru Kamiya. Tomoko went to Kaoru's side and immediately used her phone to take a selfie. Afterwards, she showed the picture to her. Kaoru, amazed with the latest technology, went to ask her more of the innovation from the future. Tomoko obliged; she showed her ID's, the money, the power bank.

"It can play music too?" Kaoru asked, astonished.

"Yes! Hmm… let's see what I have here." Tomoko searched in vain for some traditional Japanese music but found nothing.

She smiled apologetically, her left hand scratching the back of her head. "I'm sorry Miss…er…Kaoru, I do not have a traditional Japanese music here."

"Never mind. Just show me what music you have in there."

"Okay!"

"Okay?" Kaoru mimicked. "What is that?"

"Oh it is a futuristic slang meaning, 'I will' or something that affirms one's statement."

"Oh, okay!" Kaoru stated. "Did I use it right?"

Tomoko laughed, raising her right thumb up towards Kaoru. They both grinned together like long time comrades. "Here I have a music stored. Let me play it for you." Tomoko played the music of The Band Perry and One Ok Rock. Kaoru seemed to like the country songs but detested the second one. "Don't ever play the second song, it hurts my head." She remarked to the song of One Ok Rock.

"But why? It is a good song!"

"It is not! I don't like it; I'd much prefer Yahiko's shouting instead."

As if on cue, Yahiko's voice called from the outside. "Heyyyyy Ugly! Get out here and train me now!"

Kaoru and Tomoko stared at each other. "Yahiko's here!" Tomoko already knew Yahiko based from Kaoru's descriptions earlier. "Miss Kaoru, please don't let anyone know I am staying here! Rumors will start and they might find me here! I beg you please!" Tomoko pleaded to Kaoru, her eyes beginning to water again. In other circumstances, Kaoru doubted the woman's reasons but since she has already given proof that she is clearly not from this era, she needed to conceal her identity as well. She thanked the gods that no one saw her lying outside the Kamiya gate; she will use this as her method to conceal her identity. It is also possible that if the people who wanted her dead also have ability to time-travel in the past, they might be looking for a young woman with weird futuristic Western clothing.

"Do you think you can wear a male outfit?" she asked Tomoko.

"Like the kendo attire?"

"Yes! That's it, but not kendo attire. It's quite different but has the same style. Do you think you can manage to pretend as a boy? If you conceal your identity, might as well conceal your gender as well. I will hide your clothes. In that way, no one will know that you are living with me." Kaoru reasoned out.

Tomoko pondered at the thought. She never really liked the traditional male outfits in the Meiji period but what Kaoru had stated is rational. Tomoko does not know whether they are also here in this period or not. _I'll have to endure it. Dressing up a man is the same as what my folks do. I need to find the book too and with a concealed identity, they will never doubt me._ Tomoko agreed. Kaoru went to his father's former room and brought out his kimono and hakama. To conceal her identity, she let her wear her father's hat as well. "You stay there and dress up. I will hide you uniform. Yahiko usually goes to the dojo every morning so I am sure that he hasn't went to the storage house. I will deal with him, but make sure you put up your act and remember what we talked okay?"

"Yes, Ma'am."

Kaoru smiled and went out. "I will see you later. Just hide here for now. Don't let Yahiko see you or else our plan will be ruined. That brat is quite a loud mouthed punk you know."

"Thank you, Miss Kaoru." Tomoko saw a vein twitched on Kaoru's face. She gasped as she remembered what she had told her before. "Thank you Kaoru."

"Heyy Ugly get out of your room and train me now!" Yahiko called again, this time much louder.

"I'm coming there you little brat. Don't forget your assistant master still needs some time to freshen up. I'm still a woman you know." Kaoru yelled as she ran fast towards the dojo.

"No matter how you beautify yourself, you're still an ugly raccoon girl for me."

Later on, loud beatings and screams of a kid were heard from the dojo.

(Please review! Those who wait for Kenshin, it's over you will meet him in the fourth chappie! See ya! ("\\(^_^x)


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